Ahh maybe this:
What do you integrate for the "Area weighted average of velocity magnitude"? You need to integrate only the perpendicular (to the surface) component of the velocity vector - not the length of the complete velocity vector!

I tried with Velocity magnitude, X, Y and Z velocities .... still they differ.
When I calculate velocity = (volume flow rate/area) fluent and
area weighted avg of (velocity magnitude/X-vel/Y-vel/Z-vel), both differ by almost 4-5m/s

But this isn't what I wrote:
You need the perpendicular velocity component. If your surface is no "simple" cartesian surface, the cartesian (x,y,z) components won't help you.
What you need is "A dot v"!

Let the normal of the rectangle be [nx, ny, nz], and the area-weighted average of x-,y-,z- velocity be [U, V, W], then (U*nx + V*ny + W*nz) should not be differ much from the volumetric flow rate divided by the area.